Malloy was appointed Bishop of Rockford on March 20, 2012, and was consecrated as bishop on May 14, 2012, by Francis Cardinal George, Archbishop of Chicago. Malloy's predecessor, Thomas Doran, and Jerome Listecki, the Archbishop of Milwaukee, served as co-consecrators. At the time of his appointment as Bishop of Rockford, Malloy was serving as pastor of Saint Francis de Sales Parish in Lake Geneva, Wisconsin. Upon his appointment as Bishop of Rockford, Malloy joined Robert Lynch of St. Petersburg and Dennis Schnurr of the Roman Catholic Archdiocese of Cincinnati as former USCCB General Secretaries named bishops in the United States. In January 2017, Malloy sent priests of his diocese a letter stating, among other things: "In order to underscore our unity in prayer and to avoid differences between and even within parishes on this point, I ask that no Masses be celebrated 'ad orientem' without my permission." This posture is not ruled out by the General Instruction of the Roman Missal and has been recommended by Cardinal Robert Sarah of the Congregation for Divine Worship and the Discipline of the Sacraments. Sarah then met privately with Pope Francis and on 11 July the Holy See Press Office issued a statement that said that Sarah's London remarks had been "incorrectly interpreted, as if they were intended to announce new indications different to those given so far in the liturgical rules and in the words of the Pope regarding celebration facing the people and the ordinary rite of the Mass", that celebrating Mass facing the congregation was "desirable wherever possible" and not to be superseded by ad orientem. It reported that the Pope and the Cardinal were in complete agreement on these points. Malloy added: "Second, for similar reasons, in keeping with Art. 5 §1 of Summorum Pontificum, and with due regard to Art. 2 of that same document, Masses are not to be celebrated using the Extraordinary Form without my permission." Art. 5 §1 of the papal document cited says: "In parishes where a group of the faithful attached to the previous liturgical tradition stably exists, the parish priest should willingly accede to their requests to celebrate Holy Mass according to the rite of the 1962 Roman Missal. He should ensure that the good of these members of the faithful is harmonized with the ordinary pastoral care of the parish, under the governance of the bishop in accordance with Canon 392, avoiding discord and favouring the unity of the whole Church." Article 2, to which Malloy said due regard was to be given, concerns Masses said without a congregation: "In Masses celebrated without a congregation, any Catholic priest of the Latin rite, whether secular or regular, may use either the Roman Missal published in 1962 by Blessed Pope John XXIII or the Roman Missal promulgated in 1970 by Pope Paul VI, and may do so on any day, with the exception of the Easter Triduum. For such a celebration with either Missal, the priest needs no permission from the Apostolic See or from his own Ordinary."